Due to historic reasons, SeisSol write in the stdout 3 times the Simulation time: Wall time and CPU time are the same. Elapsed time (via clock_gettime) takes time at a slightly earlier point, however, the difference should be minimal.
The “total time spent in compute kernels” is the total time accumulated over all nodes without MPI communication. Basically, this measures the time in which all CPUs do some useful work.
SeisSol outputs the hardware (HW) and non-zero (NZ) flops. The first one are the flops actually calculated by the CPU, and the second one is a theoretical value that counts all flops that incorporate multiplications or additions with zero. The reason why those are distinct is that it is sometimes faster to compute a few extra zeros. E.g. we do not always have efficient routines for sparse matrix-matrix multiplication, hence we use a routine for dense matrix-matrix multiplications which is faster but adds some extra work. So the HW-GFLOP can be seen as machine utilization and the NZ-GFLOP can be seen as actual work done.
One important value, which we usually publish in our papers, is the performance in GFLOP/s/node. You can compute it with \(HW-(NZ-)GFLOP / #nodes / elapsed-time\). You can compare this value with the publications in order to see if your performance is ok.